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Dindel specifications


Unique identifier OMICS_00096
Name Dindel
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Mapped Illumina read data
Input format BAM
Output data Variant calls
Output format VCF
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Cornelis Albers <>

Publication for Dindel

Dindel citations


Exome sequencing characterizes the somatic mutation spectrum of early serrated lesions in a patient with serrated polyposis syndrome (SPS)

PMCID: 5707812
PMID: 29213343
DOI: 10.1186/s13053-017-0082-9

[…] mark duplicated reads, perform local realignment around short insertions and deletions, recalibrate the base quality scores and call snvs and short indels together with samtools version 0.1.18 and dindel version 1.01 []. on average, 104.7 million reads were uniquely mapped. 80.9% of all targeted regions were covered >30 times, with a mean coverage of 89. scripts developed in-house […]


Optimized detection of insertions/deletions (INDELs) in whole exome sequencing data

PMCID: 5549930
PMID: 28792971
DOI: 10.1371/journal.pone.0182272

[…] whole-exome sequencing (wes) data, we performed sanger sequencing for all indels called from the several calling algorithm. we compared the performance of the four algorithms (i.e. gatk, samtools, dindel, and freebayes) for indel detection from the same sample. we examined the sensitivity and ppv of gatk (90.2 and 89.5%, respectively), samtools (75.3 and 94.4%, respectively), dindel (90.1 […]


Phylogenetic analysis of metastatic progression in breast cancer using somatic mutations and copy number aberrations

PMCID: 5474888
PMID: 28429735
DOI: 10.1038/ncomms14944

[…] duplicate reads were removed using picard tools. base recalibration, local realignment around indels and snv calling were performed using the genomeanalysistoolkit (gatk). indels were called using dindel. mutations were filtered based on mapping quality, and sequencing coverage. somatic mutations were further filtered by comparison with the matched germline reference and using common variant […]


Molecular dissection of colorectal cancer in pre clinical models identifies biomarkers predicting sensitivity to EGFR inhibitors

PMCID: 5309787
PMID: 28186126
DOI: 10.1038/ncomms14262

[…] were detected using established pipelines based on varscan2 combined with rnaseq data and functional annotation of the variants based on ensembl v.70. somatic indels were detected using samtools and dindel., rna reads were aligned to hg19 using bwa and samtools. mapped reads were annotated using ensembl v70. gene expression levels were quantified in reads per kilobase of exon per million mapped […]


A human immunodeficiency syndrome caused by mutations in CARMIL2

PMCID: 5473639
PMID: 28112205
DOI: 10.1038/ncomms14209

[…] removed using samtools version 1.18 (ref. ). samtools was also used to call snps with the command: ‘mpileup –m 300 –i –g –d -c50 –s'. small insertions and deletions (indels) were identified using dindel version 1.01 (ref. ), by first identifying putative indels for each sample individually, and then re-running the dindel on the pooled set of samples from family a with the previously […]


A mutation of EPT1 (SELENOI) underlies a new disorder of Kennedy pathway phospholipid biosynthesis

PMCID: 5382949
PMID: 28052917
DOI: 10.1093/brain/aww318

[…] effect analyzer) (http://provean.jcvi.org/index.php), dbsnp (http://www.ncbi.nlm.nih.gov/snp/), 1000 genomes project (http://www.1000genomes.org/), gatk (http://www.broadinstitute.org/gatk/), dindel (https://www.sanger.ac.uk/resources/software/dindel/), snp effect predictor (http://www.ensembl.org/info/docs/tools/vep/index.html), exome aggregation consortium (exac) browser […]

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Dindel institution(s)
Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK

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